Consider all that we know from psychology about the impact of beliefs on behavior. Even when the NYT puts up a solid, grounded article, the biases of the author are going to show up. It's impossible to judge facts or events without a worldview, and it's better to be forthright about what that position is (like British newspapers, or American ones in the 19th century), than to studiously pretend that some sort of 'objective' middle ground can be reached.
This is also part of the trend where we get rid of 'jounalists' who use their intrepid fact-finding abilities to ferret out the truth, regardless of the subject at hand or their initial knowledge. Now, people can turn to actual experts (or smart lay-people) on the subject, who can communicate directly with readers instead of being intermediated by journalists. I can't imagine a world in which the only news I had about the financial crisis came from the NYT, instead of, say, commentary from Brad DeLong, Tyler Cowen, and so forth.